Sorry. My one significant foray into naval combat occurred prior to the resurgence in popularity of pirates so I haven't really looked at any of the supplements.
I will say that lower water, windwall, control winds, summon storm, call lightning, Summon water elemental/squid, warp wood, water walk, and Otiluke's Freezing Orb can seriously change combat tactics. Use of potions of alterself (aquatic race) and swimming should be common staples in the well-heeled pirate or navy's arsenal.
Barring cannons & magic, the common weapon should be archers with either longbows or crossbows for maximum range. Normal arrows for pirates trying to sieze cargo, fire arrows for navies or defenders trying to kill off an attacker. IMC many pirate ships are "combat carriers" that pack a number of viking-esque longboats. An oared vessel can outrun a sailing ship for a short period of time so these attack boats move into position to fire arrows, damage sails, or in some cases, drop "bolos" (floating barrels on long ropes that snag onto ships and create drag, slowing the ship down). Attack boats will also carry whatever offensive spell casters they might possess to get them into position and so that counter-magic doesn't damage the main ship.
Pirates will covet casters, though they probably have to luck out to find a divine caster of similar sentiment; kidnapping priests tends to be bad luck. Kidnapping a mage, however, is just peachy. Formal navies will often have arrangements with formal religion, though the nature of the arrangements will vary on the campaign setting.
Create food & water extends the range of shipping or increases the amount of cargo that can be carried. Ditto for any magic items that can do the same; Decanters of Endless Water can free up signficant cargo capacities. An Orb of Weather Control is one of the greatest treasures a captain can have.